AMBER Archive (2002)

Subject: average position of water

From: Hungie Hungie (hungie01_at_hotmail.com)
Date: Tue Jan 08 2002 - 06:28:00 CST

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Dear Amber user,

I have a trajectory of 100 ps MD simulation of a small DNA with explicit
solvent. The DNA was fixed during simulation (ibelly=1). My goal is to
equilibrate water positions.

I would like to determine something using coordinates of DNA and water
molecules. For the coordinations, I don't want to choose 1 snapshot from the
trajectory, however, I would like to use average position for the
determination.

Could anyone suggest me how to average position of waters?
I have tried to average by using ptraj with command "average" and I found
that some water molecules located within DNA. This may be water molecules
moved around DNA during simulation.

Many thanks in advance.

Regards,
Hungie

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